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The X-Ray Crystal Structures of Human

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The X-Ray Crystal Structures of Human THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 281, NO. 21, pp. 14918–14926, May 26, 2006 © 2006 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in the U.S.A. The X-ray Crystal Structures of Human ␣-Phosphomannomutase 1 Reveal the Structural Basis of Congenital Disorder of Glycosylation Type 1a* Received for publication, February 16, 2006, and in revised form, March 8, 2006 Published, JBC Papers in Press, March 15, 2006, DOI 10.1074/jbc.M601505200 Nicholas R. Silvaggi‡, Chunchun Zhang§, Zhibing Lu‡, Jianying Dai§, Debra Dunaway-Mariano§, and Karen N. Allen‡1 From the ‡Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118 and the §Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87103-0001 Congential disorder of glycosylation type 1a (CDG-1a) is a con- abnormalities. Numerous clinical genotypes have been identified, with genital disease characterized by severe defects in nervous system the range of phenotypes extending from mild to severe (9, 10). CDG-1a development. It is caused by mutations in ␣-phosphomannomutase is caused by mutations in the gene encoding ␣-phosphomannomutase (of which there are two isozymes, ␣-PMM1 and ␣-PPM2). Here we (␣-PMM) (11–13). The most common mutant, R141H (40% of disease report the x-ray crystal structures of human ␣-PMM1 in the open alleles of CDG-1a patients), has a high carrier frequency of 1/70 in the conformation, with and without the bound substrate, ␣-D-mannose general population. Individuals homozygous for this mutation have not 1-phosphate. ␣-PMM1, like most haloalkanoic acid dehalogenase been identified, suggesting that this genotype is lethal (12). superfamily (HADSF) members, consists of two domains, the cap Human ␣-PMM, which catalyzes the conversion of D-mannose and core, which open to bind substrate and then close to provide a 6-phosphate (Man-6-P) to ␣-D-mannose 1-phosphate (␣-Man-1-P) solvent-exclusive environment for catalysis. The substrate phos- (see Fig. 1) is required for GDP-mannose and dolichol-phosphate-man- phate group is observed at a positively charged site of the cap nose biosynthesis. Two isoforms are found; PMM2 is expressed in all domain, rather than at the core domain phosphoryl-transfer site tissues, whereas expression of PPM1 (65% sequence identity with 2؉ 19 defined by the Asp nucleophile and Mg cofactor. This suggests PMM2) is restricted to the brain and lungs (14). ␣-PMM belongs to the that substrate binds first to the cap and then is swept into the active haloalkanoic acid dehalogenase superfamily (HADSF), distinguishing it site upon cap closure. The orientation of the acid/base residue both structurally and mechanistically from the phosphomanno/phos- Asp21 suggests that ␣-phosphomannomutase (␣-PMM) uses a dif- phoglucomutase enzymes of the phosphohexomutase superfamily that ferent method of protecting the aspartylphosphate from hydrolysis are integral to glycolysis in prokaryotes and eukaryotes (15) and to algi- than the HADSF member ␤-phosphoglucomutase. It is hypothe- nate biosynthesis in Gram-negative bacteria (16). sized that the electrostatic repulsion of positive charges at the inter- Within the HADSF, ␣-PMM is distinguished from the bacterial face of the cap and core domains stabilizes ␣-PMM1 in the open ␤-phosphoglucomutase (␤-PGM) in its C(1) anomer specificity as well conformation and that the negatively charged substrate binds to the as in the position and fold of the cap domain which serves as a lid over cap, thereby facilitating its closure over the core domain. The two the conserved catalytic core domain. In HADSF members, wherein isozymes, ␣-PMM1 and ␣-PMM2, are shown to have a conserved phosphatases predominate, the conserved aspartate nucleophile of the active-site structure and to display similar kinetic properties. Anal- ysis of the known mutation sites in the context of the structures core domain mediates the transfer of the phosphoryl group. Remark- ␣ ␤ reveals the genotype-phenotype relationship underlying CDG-1a. ably, the -PMM and -PGM evolved independently to arrive at an adaptation of the phosphatase scaffold, which allows the aspartylphos- phate of the core domain to discriminate between solvent and the sugar- Glycoproteins play fundamental roles in humans (1, 2) where they are phosphate substrate as the phosphoryl group acceptor. ␣ active in cell recognition and adhesion, development, and homeostasis Herein we report the x-ray crystallographic structures of -PMM1 in 2ϩ (3–7). Defects in protein glycosylation lead to a variety of disease states the Mg -bound form and in complex with the substrate of the reac- ␣ known collectively as congenital disorders of glycosylation (CDG).2 The tion, -Man-1-P. These structures are analyzed in the context of the ␣ most common CDG, congenital disorder of glycosylation type 1a coordinates for uncomplexed -PMM2 deposited in the Protein Data (CDG-1a) (8), manifests in infancy with physical and developmental Bank by the Center for Eukaryotic Structural Genomics (accession code 2AMY) to identify active-site residues with roles in binding and catalysis as well as residues involved in subunit dimerization. The structure and * This work was supported by Grant GM61099 from the National Institutes of Health ␣ ␣ (NIH) (to K. N. A. and D. D.-M.) and NIH Training Grant HL07291 (to N. R. S.). The costs of kinetic analyses of -PMM1 and -PMM2 provide for the first time publication of this article were defrayed in part by the payment of page charges. This insight into how quaternary structure, stability, and catalytic efficiency article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. are altered in clinically important mutants. Section 1734 solely to indicate this fact. The atomic coordinates and structure factors (code 2FUC and 2FUE) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers Uni- EXPERIMENTAL PROCEDURES versity, New Brunswick, NJ (http://www.rcsb.org/). 1 To whom correspondence should be addressed: 715 Albany St., R-702, Boston, MA Materials—Except where indicated, all chemicals were obtained 02118. Tel.: 617-638-4398; Fax: 617-638-4273; E-mail: [email protected]. 2 The abbreviations used are: CDG, congenital disorders of glycosylation; CDG-1a, con- from Sigma. Primers, T4 DNA ligase, and restriction enzymes were genital disorder of glycosylation type 1a; ␣-PMM, ␣-phosphomannomutase; ␣-Man- from Invitrogen. The Geneclean spin kit and the Qiaprep spin miniprep ␣ 1-P, -D-mannose 1-phosphate; HADSF, haloalkanoic acid dehalogenase superfamily; kit were from Qiagen. Host cells were purchased from Novagen. The ␤-PGM, ␤-phosphoglucomutase, ␣-PMM1⅐Man-1-P, ␣-PMM1 in complex with ␣-D- mannose 1-phosphate; SeMet, selenomethionine; DTT, dithiothreitol. Biolmol green phosphate assay kit was purchased from Biolmol 14918 JOURNAL OF BIOLOGICAL CHEMISTRY VOLUME 281•NUMBER 21•MAY 26, 2006 Structural Basis of CDG1a FIGURE 1. Scheme for the reaction catalyzed by human ␣-phosphomannomutase. The C-1 and C-6 positions on the hexose ring are labeled in the first step. ␣ ϫ Research Laboratories Inc. The -mannose 1,6-bisphosphate used in pared by mixing 200 ml of 20 M9(10gofNH4Cl, 30 g of KH2PO4,60g the kinetic assays was prepared according to published procedure (13). of Na2HPO4, 500 ml of H2O, pH 7.5), 20 ml of amino acid mix I (the 20 Cloning, Expression, and Purification—The cDNA encoding the standard amino acids excluding Met, Tyr, Trp, and Phe, each at 4 ␣-PMM1 gene was purified from the host cells purchased from ATCC mg/ml), 40 ml of amino acid mix II (Tyr, Trp, and Phe, each at 2 mg/ml Ј (ATCC 7483527). Oligonucleotide primers (5 -CGCGGACCTG- in distilled/deionized H2O, pH 9.0), 1 ml of vitamin mixture (riboflavin, CAGCCATGGCA, and 5Ј-ACACACAGATGTGGGATCCGGTCA), niacinamide, pyridoxine monohydrochloride, and thiamine, each at 1 containing the restriction endonuclease cleavage sites NcoI and BamHI mg/ml), 4 ml of 1 M MgSO4, 4 ml of 12.5 mg/ml FeSO4,20mlof40% (underlined), were used to amplify the ␣-PMM1 open reading frame. (w/w) glucose, and 4 ml of 10 mg/ml selenomethionine in a final volume The open reading frame of ␣-PMM2 was obtained from the Mamma- of 2 liters. Chloramphenicol (16.5 mg/liter) and kanamycin (50 mg/liter) lian Genome Collection, Homo sapiens, and amplified using primers were added to the culture. The culture was grown at 30 °C with shaking Ј containing NdeI and a BamHI restriction sites (underlined) (5 - at 200 rpm until the A reached 0.8–1.1 (24 h), at which point Ј Ј 600 GAAACTGGGCATATGGCAGCGCCT-3 and 5 -TGTGGGAG- ␣-PMM1 expression was induced by adding IPTG to a final concentra- Ј ␣ ␣ GATCCTCGGCTCT-3 ). The -PMM1 and -PMM2 genes were tion of 0.4 mM. The cells were grown for an additional 10 h at 25 °C and ϩ ϩ cloned into pET-28b( ) or pET-23b( ) vectors (Stratagene), respec- harvested by centrifugation. The protein was purified using the proce- ϩ ϩ tively. The ligation products (pET-28b( )-pmm1 or pET-23b( )- dure described above, except that the DTT concentration was increased pmm2) were used to transform Escherichia coli JM109 competent cells. to 10 mM, and 1 mM EDTA was added throughout. The purified plasmids were sequenced by the Tufts University Core The purification of ␣-PMM2 was similar to that of ␣-PMM1 with Facility. a few modifications. The cell pellet from a 10-liter culture of E. coli ␣-PMM-1 was purified from E. coli RosettaTM (DE3) cells containing RosettaTM (DE3) cells (30 g) containing the pET-23b(ϩ)-pmm2 plas- the pET-28b(ϩ)-pmm1 plasmid. Transformed cells (4L) were grown at mid was suspended in 300 ml of Tris-HCl buffer (pH 8.5, 10 mM MgCl , 37 °C in Luria broth (or minimal medium containing selenomethionine) 2 5mM DTT). The cell lysate was loaded directly onto a Q-Sepharose containing 50 ␮g/ml ampicillin and induced for 4 h with 0.4 mM isopro- column (Amersham Biosciences), pre-equilibrated with Tris-HCl pyl ␤-D-thiogalactopyranoside.
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